The ITS2 Database III—sequences and structures for phylogeny

Abstract

The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160 000 correct full length and more than 50 000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses.

The blood alga: phylogeny ofHaematococcus(Chlorophyceae) inferred from ribosomal RNA gene sequence data

“…and Haematococcus pluvialis (SAG 34-1h) were directly folded with the help of the RNAstructure program (Mathews et al, 2004) and subsequently manually corrected. The predicted ITS2 secondary structure of Haematococcus droebakensis was obtained from the ITS2 database Selig et al, 2008;Koetschan et al, 2010Koetschan et al, , 2012, whereas the secondary structures of Stephanosphaera pluvialis and the additional 42 strains of Haematococcus (Table S2) were predicted by homology modelling , using either Stephanosphaera sp. (for S. pluvialis) or Haematococcus pluvialis SAG 34-1h (for the Haematococcus) strains as a template.…”

Molecular phylogeny of the Myzorhynchella Section of Anopheles (Nyssorhynchus) (Diptera: Culicidae): genetic support for recently described and resurrected species

“…Template ITS2 secondary structure was then predicted for An. antunesi RJ036 with Predict ITS2 Structure in the ITS2 Database (Koetschan et al 2010). The remaining secondary structures were modelled at this source with Custom Modelling using the predicted An.…”

The inhibitory effect of a non-yessotoxin-producing dinoflagellate, Lingulodinium polyedrum (Stein) Dodge, towards Vibrio vulnificus and Staphylococcus aureus

“…The alignment included 593 positions. Separate analyses of ITS2 were also performed as in Koetschan et al (2010). The ITS analyses were rooted with seven outgroup taxa (Table 1).…”

“…5.7 (Mathews et al, 2004). Our strain of L. polyedrum from Manzanillo (Table 1) was used as a template for homologous modeling of other L. polyedrum strains through ITS2 Database (http:// its2-old.bioapps.biozentrum.uni-wuerzburg.de/ cgi-bin/index.pl?custom) (Schultz et al, 2006;Selig, Wolf, Mülle, Dandekar, & Schultz, 2008;Koetschan et al, 2010). Helices were recognized by comparing the ITS2 regions of several L. polyedrum sequences obtained from the above ITS2 database.…”